The Enterprise is in danger of a reactor breach, so Archer frees Malcolm from the brig and tells him to bring Trip. Malcolm and T'Pol work to merge the warp fields of Enterprise and Columbia, then Captain Hernandez hails the Enterprise to tell them that the ship has matched Enterprise's speed and trajectory. Columbia spins around, then Malcolm sends a tether so that Trip can go back to Enterprise, and despite a bit of a struggle and the tether eventually breaking off, he succeeds.
Once Trip is onboard, he thinks of a solution: purge the subroutines and shut down the engine. He notices the MACOs outside the launch bay and asks Malcolm for confirmation, but Malcolm only confuses him further by saying he had a "misunderstanding" with Archer before going back to the brig. Hernandez tells Archer that they've routed everything they can to the warp field, so Archer gives Trip the go-ahead, and he starts the shut-down procedure, which succeeds. Afterwards, Archer asks Columbia to stay around.
On Qu'Vat Colony, Dr. Antaak finds Phlox in his cell. Phlox, who refuses to create genetically-engineered soldiers, tells Antaak to 'end it' and contact Starfleet. Antaak has been studying Phlox's data and has found a flaw in the virus. Phlox tells him that he's also noticed it, but K'Vagh would refuse treatment. Antaak suggests they do it without telling the general.
The Enterprise, assisted by the Columbia, is searching for Phlox. Malcolm is taken to his quarters, where Archer has been going through Malcolm's files to look for info on Harris, but has found none. Malcolm, claiming to be following orders, doesn't give him any information, so Archer, determined to identify Harris, tells Malcolm to contact him himself.
Antaak and Phlox compare family histories, with Antaak noting that his dad disowned him once he became a healer, and blaming himself for the virus. The Bird-of-Prey with the Klingon Augments arrives back at the colony, and Laneth says that the Enterprise was destroyed. When K'Vagh sees that his son is missing, Laneth claims that the humans killed him.
K'Vagh checks up on the doctors, who are making good progress. Phlox claims to have found the "switch" that will "turn off" the virus and it will be ready within the hour. K'Vagh contacts Krell, who tells him that the Klingon High Council has shut down the project. K'Vagh argues that their research will be lost if the colony is destroyed, so Krell gives him three hours or it will be.
Back on Enterprise, Trip says he will assist the ship's new chief engineer Kelby. He then asks why Malcolm is in the brig, but Archer says he can't say. T'Pol takes Trip to Columbia and they awkwardly ask each other if they've had insomnia, which they haven't. Meanwhile, Phlox asks K'Vagh how his son got the virus, and he replies that it was tested on him after they ran out of prisoners to test it on.
Malcolm eats, but his neighbour, a Klingon named Marab, refuses to eat. Malcolm asks why Klingons are warlike, but Marab says that one could be imprisoned or killed for asking questions like that. Laneth and her shipmates are now in poor condition due to the virus. K'Vagh tells them that Phlox is working on a cure, and Laneth wonders if her appearance will change and worries that (since she felt fear for the first time since childhood) she's becoming emotionally weak.
Archer and Porthos are in his quarters, when Harris contacts him and tells him that Phlox is on an important mission. Harris directs Archer to Article 14, Section 31 of the Starfleet Charter. Archer guesses the Klingons are involved, but Harris wants to talk about Malcolm instead. Archer says that Malcolm was put into an "impossible situation", but Harris says that there's more to the situation than one captain and one ship and if Phlox fails, the results could be devastating. Phlox holds four strains, one of which has the cure, but he doesn't know which. Unfortunately, determining which one would take a week, so he must infect four healthy Klingons. K'Vagh tells him to infect him, Antaak, and two guards.
In Archer's ready room, Malcolm explains why he joined Section 31. He joined them as an ensign, but hasn't done any other work for them since before joining the Enterprise crew. Archer shows him Marab's medical scans and believes it's a botched military experiment. Harris believed a cure needed to be found to make the Empire more stable. Malcolm confesses to wanting to tell Archer, who tells him to decide where his loyalties lie. Malcolm doesn't know where Phlox is, but does know that there's a genetic research facility on Qu'Vat Colony.
Archer reinstates Malcolm and they head towards Qu'Vat. Meanwhile, Phlox asks K'Vagh why he attempted the Augment project when Soong failed. K'Vagh says that Soong's only failure was making too few Augments and that Klingons have discipline (even though, as Phlox points out, Augments don't). Phlox injects K'Vagh, then the Klingons start drinking bloodwine, which Phlox turns down, since he never drinks at work.
Archer interrogates a sickly Marab, who agrees to help only when Archer suggests he agree to help his own people. Antaak enters, noting that the guards are becoming sick, and Phlox scans him, revealing that he's also sick (and K'Vagh has the cure), but there's hope— if Phlox can work quickly enough, Antaak and the guards can be cured.
Harris contacts Krell, saying that Krell failed to stop Enterprise and Columbia. Krell orders Harris to withdraw the ships, but Harris says no since he lacks the necessary authority. Krell wants to destroy the ships, but Harris reminds him of the arrangement. However, Krell has no problem with breaking his promise. As Antaak prepares to extract the cure from K'Vagh, Archer and Marab enter. Archer wants Phlox back, and Phlox asks for a few more hours to perfect the cure. Ka'Vagh is angry that Phlox isn't helping perfect the Augment genome, but Phlox admits to lying about intending to do that.
Malcolm detects the three Klingon warships, but the communication line to Columbia isn't working. An alarm goes off on the surface, and Archer tries to contact Enterprise but fails. Krell, despite Archer's objections, says that the colony will be eradicated, claiming to have a more "effective" solution. Phlox tells Krell about the anti-virus, but Krell declares the Enterprise and Columbia property of the Klingon Empire.
Krell orders his tactical officer to proceed, so his battle cruiser starts firing. Enterprise tries to stop the ship, but is hindered by two Birds-of-Prey. Phlox then explains that he will find the cure quickly with a human "host", so Archer volunteers. Columbia, whose shields are failing, manages to disable one of the Klingon ships, while Hoshi cuts through the jamming signal. Archer is unavailable, so she talks to Phlox instead, who asks them to protect the colony and Malcolm to increase power to the hull plating. Meanwhile, Archer is growing ridges on his head.
The Klingon battle cruiser tries to throw Enterprise off, but it doesn't work. T'Pol asks Hernandez for assistance, but she can't help as Columbia has lost its weapons. Archer escapes from his restraints, so Ka'Vagh holds him down while Phlox extracts the antibodies. Antaak sends a container of viruses to Krell's ship, thereby infecting his crew.
Phlox tells Krell that the container contains viruses, but Krell doesn't believe him. Phlox tells him to either check the sensors or wait half an hour when the symptoms start, but Krell still doesn't believe him. Phlox says that if the cure is destroyed, he'll die from the virus, unless he orders the ships to stand down, which finally makes Krell cave in.
Antaak and Archer recover in sickbay, although Antaak now has a smooth head and Archer still has ridges and is having cravings for gagh. Archer thanks Hernandez for her help, and Trip says he will be sticking around for a while longer. Malcolm reads in his quarters, when Harris enters and contacts him to thank him. Malcolm tells Harris to never contact him again since he answers to one man alone: Jonathan Archer.
Tropes in this episode include:
- Big Damn Heroes: With Enterprise in a situation straight out of Speed, Columbia comes to the rescue.
- Blessed with Suck: Bioaugmentation turns Klingon warriors into Super Soldiers, at the cost of human appearance and emotions.Laneth: How do you expect us to return home looking like this? We will be outcasts. There will be no place for us in the Empire.K'Vagh: Your heart is still Klingon.Laneth: Are you certain of that? During the battle with the Starfleet ship I felt fear for the first time since I was a child. I wasn't alone. I could see it in the eyes of the others. We've become like them. Weak, cowardly. It would be better for us to die.
- Combat Pragmatist: Phlox has no problem using a bio-weapon against Krell and his crew, though he does promise to cure them if they would please stop shooting.
- Continuity Nod: Back in "Inquisition," Sloane told Bashir that Section 31 was part of the original Starfleet charter, which we learn to be "Article 14, Section 31." Specifically, it allows "the rules to be bent" during times of extraordinary threat.
- Continuity Snarl: A computer graphic of Enterprise and Columbia pulling their maneuver includes the "USS" prefix, even though Starfleet doesn't use it until The Federation is formed.
- A Father to His Men: General K'Vagh does care for his warriors who volunteered to undergo the genetic modifications and promises that they'll be cured. (And since one of those warriors is his own son, this trope applies literally.)
- I Have No Son!: Apparently, once Antaak became a doctor, his father disowned him.
- I Lied:
- Krell has no intention of honoring his agreement with Harris.Harris: We had an arrangement!
Krell: You did what I wanted. I don't need you anymore.
Harris: You agreed that both our governments would benefit if the two of us worked together.
Krell: And you believed me. - Phlox also cheerfully says this when he reveals to the General that he was curing the disease rather than perfecting the augment genome.Phlox: Captain. I need a little more time to cure this plague.
K'Vagh: Cure? You were supposed to perfect the Augment genome!
Phlox: I lied.
- Krell has no intention of honoring his agreement with Harris.
- Improvised Weapon: Phlox beams a canister with the virus onto Krell's ship so that he'll be forced to stop his attack and accept the cure — though how he beams something on board a starship with its shields up is something of a Plot Hole (albeit one that's happened before).
- It's All My Fault: Antaak blames himself for the plague.
- It's the Only Way to Be Sure: The Klingons nearly destroy Qu'vat colony to stop the spread of the virus.
- Klingon Scientists Get No Respect: Antaak says his family disowned him when he decided to become a healer rather than a warrior.
- You Have Failed Me: Phlox warns Antaak that they might suffer this fate if they don't produce Klingon augments as promised.
